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Nucleic Acids Res. 2016 Jan 4;44(D1):D415-22. doi: 10.1093/nar/gkv1236. Epub 2015 Nov 17.

iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics.

Author information

1
Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA 15213, USA.
2
Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 300, Taiwan.
3
Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 300, Taiwan bahar@pitt.edu.
4
Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA 15213, USA lwyang@life.nthu.edu.tw.

Abstract

Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0 http://gnmdb.csb.pitt.edu/, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.

PMID:
26582920
PMCID:
PMC4702874
DOI:
10.1093/nar/gkv1236
[Indexed for MEDLINE]
Free PMC Article
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